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. 2023 Jul;29(7):1069–1076. doi: 10.1261/rna.079583.123

FIGURE 1.

FIGURE 1.

(A) A standard wobble G•U pair (from PDB 1HQ1, Batey et al. 2001) with a water molecule in the minor groove (red sphere) and a hydrated potassium ion (purple sphere) in the major groove. All distances are in Å and between the heavy atoms. The distance between the two C1′ carbon atoms is 10.7 Å (values between 10.4 Å and 10.7 Å are commonly observed). (B) The observed G•U pair between G3 and modified U34* in the ternary complex between the ribosomal A site, the anticodon loop of the A-tRNA and the mRNA (from PDB 5E81, Rozov et al. 2016a). The tRNA U34* is modified in 5-methylaminomethyl-2-thioUridine. The distance between the two C1′ carbon atoms is 11.4 Å. (C) Possible electronic structure of the modified U34* where X at position 2 is S and R at position 5 is methylaminomethyl, probably charged and thus forming a zwitterion. The negative charge may be delocalized between the N3 and S2. For chemical data and a discussion, see Sochacka et al. (2015, 2017).